def _apply_log_status(self, log_status): """Apply an RDKit log status.""" for k, v in log_status.items(): if v is True: rdBase.EnableLog(k) else: rdBase.DisableLog(k)
def getTestFrame(): rdBase.DisableLog('rdApp.error') sdfFile = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', 'pandas_load.sdf.gz') df = PandasTools.LoadSDF(sdfFile, smilesName='SMILES') rdBase.EnableLog('rdApp.error') return df
def enable_rdkit_log(): """ Enables RDkit logging. :return: """ if rdb is None: raise ImportError('`enable_rdkit_log` requires RDkit.') rdb.EnableLog('rdApp.error')
def test_load_gzip_file(self): rdBase.DisableLog('rdApp.error') df = PandasTools.LoadSDF(self.gz_filename) rdBase.EnableLog('rdApp.error') self.assertEqual(len(df), 13) # The molecule with index 1 is invalid, so it should be missing form the index self.assertEqual(list(df.index), [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13])
def test_isValidRingCut(self): rdBase.DisableLog('rdApp.error') self.assertEqual(FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]CCC[*]')), False) self.assertEqual(FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]C1CC1[*]')), True) self.assertEqual(FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]c1ccccc1[*]')), True) self.assertEqual( FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]cccc[*]', sanitize=False)), False) rdBase.EnableLog('rdApp.error')
def enable_rdkit_log(): rdBase.EnableLog('rdApp.*')
import fileinput import logging import numpy as np import re from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate from rdkit.Chem import Draw from rdkit.Chem.Draw.MolDrawing import DrawingOptions #logging.basicConfig(filename='example.log',level=logging.CRITICAL) from .molecule_properties_tools import stdout_redirected, remove_isotopes rdBase.DisableLog('rdApp.debbug') rdBase.DisableLog('rdApp.info') rdBase.DisableLog('rdApp.warning') rdBase.EnableLog('rdApp.error') rdBase.EnableLog('rdApp.critical') import logging nometals = { 'H', 'He', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Si', 'P', 'S', 'Cl', 'Ar', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Te', 'I', 'Xe', 'At', 'Rn' } def write_entry(line, fileh, serial): if serial < 99999: newserial = "%5d" % serial else: newserial = "*****"
def enable_rdkit_log(): """Enable all rdkit logs.""" for log_level in RDLogger._levels: rdBase.EnableLog(log_level)
def disable_rdkit_log(): rdBase.DisableLog('rdApp.error') try: yield finally: rdBase.EnableLog('rdApp.error')
def enable_rdkit_log(): """tbd""" rdBase.EnableLog('rdApp.*')
def setUpClass(cls): rdBase.LogToCppStreams() rdBase.WrapLogs() rdBase.EnableLog('rdApp.debug') rdBase.EnableLog('rdApp.info')